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Nature. 2015 Aug 6;524(7563):97-101. doi: 10.1038/nature14594. Epub 2015 Jun 17.

Temporal and spatial analysis of the 2014-2015 Ebola virus outbreak in West Africa.

Carroll MW1, Matthews DA2, Hiscox JA3, Elmore MJ4, Pollakis G3, Rambaut A5, Hewson R6, García-Dorival I3, Bore JA7, Koundouno R7, Abdellati S8, Afrough B9, Aiyepada J10, Akhilomen P10, Asogun D10, Atkinson B9, Badusche M11, Bah A12, Bate S9, Baumann J13, Becker D14, Becker-Ziaja B11, Bocquin A15, Borremans B16, Bosworth A17, Boettcher JP18, Cannas A19, Carletti F19, Castilletti C19, Clark S9, Colavita F19, Diederich S20, Donatus A10, Duraffour S21, Ehichioya D22, Ellerbrok H18, Fernandez-Garcia MD23, Fizet A24, Fleischmann E25, Gryseels S16, Hermelink A18, Hinzmann J18, Hopf-Guevara U18, Ighodalo Y10, Jameson L9, Kelterbaum A14, Kis Z26, Kloth S18, Kohl C18, Korva M27, Kraus A28, Kuisma E9, Kurth A18, Liedigk B11, Logue CH9, Lüdtke A29, Maes P30, McCowen J9, Mély S15, Mertens M20, Meschi S19, Meyer B31, Michel J18, Molkenthin P25, Muñoz-Fontela C29, Muth D31, Newman EN9, Ngabo D9, Oestereich L11, Okosun J10, Olokor T10, Omiunu R10, Omomoh E10, Pallasch E11, Pályi B26, Portmann J32, Pottage T9, Pratt C9, Priesnitz S33, Quartu S19, Rappe J34, Repits J35, Richter M18, Rudolf M11, Sachse A18, Schmidt KM18, Schudt G14, Strecker T14, Thom R9, Thomas S9, Tobin E10, Tolley H9, Trautner J36, Vermoesen T8, Vitoriano I9, Wagner M25, Wolff S14, Yue C18, Capobianchi MR19, Kretschmer B37, Hall Y4, Kenny JG38, Rickett NY3, Dudas G39, Coltart CE40, Kerber R11, Steer D41, Wright C42, Senyah F4, Keita S43, Drury P44, Diallo B45, de Clerck H46, Van Herp M46, Sprecher A46, Traore A47, Diakite M48, Konde MK49, Koivogui L50, Magassouba N51, Avšič-Županc T27, Nitsche A18, Strasser M32, Ippolito G19, Becker S14, Stoecker K25, Gabriel M11, Raoul H52, Di Caro A19, Wölfel R25, Formenty P44, Günther S11.

Author information

1
1] Public Health England, Porton Down, Wiltshire SP4 0JG, UK [2] The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, D-20359 Hamburg, Germany [3] University of Southampton, South General Hospital, Southampton SO16 6YD, UK.
2
Department of Cellular and Molecular Medicine, School of Medical Sciences, University of Bristol, Bristol BS8 1TD, UK.
3
Institute of Infection and Global Health, University of Liverpool, Liverpool L69 2BE, UK.
4
Public Health England, Porton Down, Wiltshire SP4 0JG, UK.
5
1] Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 2FL, UK [2] Fogarty International Center, National Institutes of Health, Bethesda, Maryland 20892, USA [3] Centre for Immunology, Infection and Evolution, University of Edinburgh, Edinburgh EH9 2FL, UK.
6
1] Public Health England, Porton Down, Wiltshire SP4 0JG, UK [2] The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, D-20359 Hamburg, Germany [3] London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK.
7
1] The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, D-20359 Hamburg, Germany [2] Université Gamal Abdel Nasser de Conakry, Laboratoire des Fièvres Hémorragiques en Guinée, Conakry, Guinea [3] Institut National de Santé Publique, Conakry, Guinea.
8
1] The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, D-20359 Hamburg, Germany [2] Institute of Tropical Medicine, B-2000 Antwerp, Belgium.
9
1] Public Health England, Porton Down, Wiltshire SP4 0JG, UK [2] The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, D-20359 Hamburg, Germany.
10
1] The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, D-20359 Hamburg, Germany [2] Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria.
11
1] The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, D-20359 Hamburg, Germany [2] Bernhard Nocht Institute for Tropical Medicine, D-20359 Hamburg, Germany [3] German Centre for Infection Research (DZIF), 38124 Braunschweig, Germany.
12
1] The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, D-20359 Hamburg, Germany [2] Swiss Tropical and Public Health Institute, University of Basel, CH-4002 Basel, Switzerland.
13
1] The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, D-20359 Hamburg, Germany [2] Bernhard Nocht Institute for Tropical Medicine, D-20359 Hamburg, Germany.
14
1] The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, D-20359 Hamburg, Germany [2] German Centre for Infection Research (DZIF), 38124 Braunschweig, Germany [3] Institute of Virology, Philipps University Marburg, 35043 Marburg, Germany.
15
1] The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, D-20359 Hamburg, Germany [2] National Reference Center for Viral Hemorrhagic Fevers, 69365 Lyon, France [3] Laboratoire P4 Inserm-Jean Mérieux, US003 Inserm, 69365 Lyon, France.
16
1] The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, D-20359 Hamburg, Germany [2] Department of Biology, University of Antwerp, B-2020 Antwerp, Belgium.
17
1] Public Health England, Porton Down, Wiltshire SP4 0JG, UK [2] The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, D-20359 Hamburg, Germany [3] Institute of Infection and Global Health, University of Liverpool, Liverpool L69 2BE, UK.
18
1] The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, D-20359 Hamburg, Germany [2] Robert Koch Institute, 13353 Berlin, Germany.
19
1] The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, D-20359 Hamburg, Germany [2] National Institute for Infectious Diseases (INMI) Lazzaro Spallanzani, 00149 Rome, Italy.
20
1] The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, D-20359 Hamburg, Germany [2] German Centre for Infection Research (DZIF), 38124 Braunschweig, Germany [3] Friedrich Loeffler Institute, Federal Research Institute for Animal Health, 17493 Greifswald, Insel Riems, Germany.
21
1] The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, D-20359 Hamburg, Germany [2] Bernhard Nocht Institute for Tropical Medicine, D-20359 Hamburg, Germany [3] KU Leuven Rega institute, B-3000 Leuven, Belgium.
22
1] The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, D-20359 Hamburg, Germany [2] Bernhard Nocht Institute for Tropical Medicine, D-20359 Hamburg, Germany [3] Redeemer's University, Osun State, Nigeria.
23
1] The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, D-20359 Hamburg, Germany [2] Centro Nacional de Microbiologia, Instituto de Salud Carlos III, 28029 Madrid, Spain.
24
1] The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, D-20359 Hamburg, Germany [2] National Reference Center for Viral Hemorrhagic Fevers, 69365 Lyon, France [3] Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, 69365 Lyon, France.
25
1] The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, D-20359 Hamburg, Germany [2] German Centre for Infection Research (DZIF), 38124 Braunschweig, Germany [3] Bundeswehr Institute of Microbiology, 80937 Munich, Germany.
26
1] The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, D-20359 Hamburg, Germany [2] National Center for Epidemiology, National Biosafety Laboratory, H-1097 Budapest, Hungary.
27
1] The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, D-20359 Hamburg, Germany [2] Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, SI-1000 Ljubljana, Slovenia.
28
1] The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, D-20359 Hamburg, Germany [2] Public Health Agency of Sweden, 171 82 Solna, Sweden.
29
1] The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, D-20359 Hamburg, Germany [2] German Centre for Infection Research (DZIF), 38124 Braunschweig, Germany [3] Heinrich Pette Institute - Leibniz Institute for Experimental Virology, 20251 Hamburg, Germany.
30
1] The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, D-20359 Hamburg, Germany [2] KU Leuven Rega institute, B-3000 Leuven, Belgium.
31
1] The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, D-20359 Hamburg, Germany [2] German Centre for Infection Research (DZIF), 38124 Braunschweig, Germany [3] Institute of Virology, University of Bonn, 53127 Bonn, Germany.
32
1] The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, D-20359 Hamburg, Germany [2] Federal Office for Civil Protection, Spiez Laboratory, CH-3700 Spiez, Switzerland.
33
1] The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, D-20359 Hamburg, Germany [2] Bundeswehr Hospital, 22049 Hamburg, Germany.
34
1] The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, D-20359 Hamburg, Germany [2] Institute of Virology and Immunology, CH-3147 Mittelhäusern, Switzerland.
35
1] The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, D-20359 Hamburg, Germany [2] Janssen-Cilag, SE-192 07 Sollentuna, Sweden.
36
1] The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, D-20359 Hamburg, Germany [2] Thünen Institute, D-22767 Hamburg, Germany.
37
Eurice - European Research and Project Office GmbH, 10115 Berlin, Germany.
38
Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
39
Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 2FL, UK.
40
Department of Infection and Population Health, University College London, London WC1E 6JB, UK.
41
Research IT, University of Bristol, Bristol BS8 1HH, UK.
42
Advanced Computing Research Centre, University of Bristol, Bristol BS8 1HH, UK.
43
Ministry of Health Guinea, Conakry, Guinea.
44
World Health Organization, 1211 Geneva 27, Switzerland.
45
World Health Organization, Conakry, Guinea.
46
Médecins Sans Frontières, B-1050 Brussels, Belgium.
47
Section Prévention et Lutte contre la Maladie à la Direction Préfectorale de la Santé de Guéckédou, Guéckédou, Guinea.
48
Université Gamal Abdel Nasser de Conakry, CHU Donka, Conakry, Guinea.
49
Health and Sustainable Development Foundation, Conakry, Guinea.
50
Institut National de Santé Publique, Conakry, Guinea.
51
Université Gamal Abdel Nasser de Conakry, Laboratoire des Fièvres Hémorragiques en Guinée, Conakry, Guinea.
52
1] The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, D-20359 Hamburg, Germany [2] Laboratoire P4 Inserm-Jean Mérieux, US003 Inserm, 69365 Lyon, France.

Abstract

West Africa is currently witnessing the most extensive Ebola virus (EBOV) outbreak so far recorded. Until now, there have been 27,013 reported cases and 11,134 deaths. The origin of the virus is thought to have been a zoonotic transmission from a bat to a two-year-old boy in December 2013 (ref. 2). From this index case the virus was spread by human-to-human contact throughout Guinea, Sierra Leone and Liberia. However, the origin of the particular virus in each country and time of transmission is not known and currently relies on epidemiological analysis, which may be unreliable owing to the difficulties of obtaining patient information. Here we trace the genetic evolution of EBOV in the current outbreak that has resulted in multiple lineages. Deep sequencing of 179 patient samples processed by the European Mobile Laboratory, the first diagnostics unit to be deployed to the epicentre of the outbreak in Guinea, reveals an epidemiological and evolutionary history of the epidemic from March 2014 to January 2015. Analysis of EBOV genome evolution has also benefited from a similar sequencing effort of patient samples from Sierra Leone. Our results confirm that the EBOV from Guinea moved into Sierra Leone, most likely in April or early May. The viruses of the Guinea/Sierra Leone lineage mixed around June/July 2014. Viral sequences covering August, September and October 2014 indicate that this lineage evolved independently within Guinea. These data can be used in conjunction with epidemiological information to test retrospectively the effectiveness of control measures, and provides an unprecedented window into the evolution of an ongoing viral haemorrhagic fever outbreak.

PMID:
26083749
DOI:
10.1038/nature14594
[Indexed for MEDLINE]

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